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Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis

Research datakeyboard_double_arrow_right Dataset 23 Dec 2019 English Publisher:Zenodo

Authors: Ćuković, Katarina; Dragićević, Milan; Bogdanović, Milica; Paunović, Danijela; Giurato, Giorgio; Filipović, Biljana; Subotić, Angelina; +2 Authors

doi: 10.5281/zenodo.3591805 , 10.5281/zenodo.3591804

Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis

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Abstract

Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) were sequenced and de novo assembled using Trinity . CE_Assembly.tar.gz - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes. CE_Assembly_fpkm.tar.gz - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues. nt.db_CE_assembly.tar.gz - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10-3. swissprot.db_CE_assembly.tar.gz - annotation of assembled transcripts by mapping them against NCBI nucleotide (swissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10-3. pfam30.db_CE_assembly.tar.gz - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10-3.

Related Organizations

Institute for Biological Research “Siniša Stanković”
Serbia
Università degli studi di Salerno
Italy
University of Belgrade
Serbia
University of Belgrade, Institute of Physics
Serbia
Institute for Multidisciplinary Research
Serbia

Keywords

Centaurium erythraea, morphogenesis, transcriptome assembly, RNA-Seq

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